Doctor Whooves: The Defeat
by Time Turner96
Summary: "I control both the sun and moon, but why do they hurt, Doctor?"-Bad Wolf. For years, The Doctor has pondered the true meaning of these words, until he came to Ponyville. Now, he's locked himself up in the TARDIS library to search for answers and won't come out. Meanwhile, a certain cross-eyed mare discovers a plot that threatens Equestria and all its subjects. His defeat is coming
1. Prologue

**Prologue**

"**I**_** can control the Sun and the Moon; but why do they hurt? Doctor, why do they hurt?"  
-Bad Wolf**_

That metaphor haunted The Doctor, who didn't understand it's meaning until he came to Equestria. When he travelled alone, he would research on the Night and Day cycles the two princesses had control over here. The minutes he spent researching turned into hours, and the hours turned into days. Derpy Hooves eventually became concerned about his well-being, so she did the only smart thing she could think of and requested an audience with the princesses themselves. Denial after denial came through, until one day a letter arrived that read as followed:

"_Dear Derpy Hooves,_

_ I, Princess Celestia along with my sister, Princess Luna have received the many requests to be granted an audience with us. As much as we wish to help you in the matter that has arisen, we simply cannot have you come to Canterlot. A threat has been claimed on our lives and we must take every precaution to prevent our untimely deaths."_

_With much sorrow and regret,_

_ Princesses Luna and Celestia_

_ P.S. On a more private note, we are fully aware that you are a companion of The Doctor, and it has also occurred to us the request for our audience was to seek help for whatever danger he is in. Listen, whatever is wrong; please try to seek help for The Doctor as much as you can._

After reading the letter, this gave Derpy an idea. "_Tomorrow, I'll go to the library and see if Twilight is there. For now, I'm going to find out what he's been researching this whole time" _the mare thought to herself.

_The next morning, in the TARDIS…_

"Doctor, are you in here?" She said as she was approaching the library. When she approached the doors, Derpy could hear mumbling of some sort and slightly opened the door. As soon as she did that, the mumbling stopped and she heard somepony get up from a chair and walk towards the door. "Doctor, I'm very worried about you." She paused for a moment, expecting a reply, but there was none so she continued. "It's been days since you first went in there." Derpy opened the door all the way this time, and before her stood The Doctor, but with a dirty coat, baggy eyes, and ruffled mane. She would have never recognized him if it weren't for his golden eyes, gazing with hope stronger than ever. "Not to worry, Ditzy!" The Doctor said "My name's Derpy…" "Right, Ditzy! What I've been doing in here is researching something important and I think it corresponds with your rulers' ability to raise and lower the sun and moon. Now if I only had the proper books…"

Derpy got a brilliant idea to get The Doctor to come with her to see Twilight Sparkle. '_if I can convince him there are better research materials at the library in Ponyville, maybe he'll come with me and we can talk about what it is that's so important that he had to abandon Me, Dinky and the rest of his friends'. _"Doctor, maybe there's a book in the Ponyville that can help you with your research!" She said. "Great idea, Ditzy! Let's go ask Twilight if there's anything that can help us find what I'm looking for." "Oh, it's Princess Twilight, now. You probably don't remember because during that time we had to hide your identity from the Krillitanes." So the Doctor and Derpy went to the library, which would be the start of a path neither of them could predict; One that would change their lives forever.

_A few moments later at the Ponyville Library…_

"Derpy, I'm glad you came by! You said there was something wrong with the Doctor, right?" Twilight asked. "(In a hushed tone) keep your voice down! I convinced him there were research materials on the sun and moon cycles here; He doesn't know why I really brought him. The Doctor's in a bad state, Twilight. Just look at him! His mane is knotted up and his coat looks like it hasn't been washed in months! Please try to help him, okay? For now, let's keep up the act to bide us some time." The purple mare nodded in agreement. "I have the materials right here for you Doc-" Suddenly, The Doctor became giddy when he saw the new wings Princess Twilight adorned on her back "You're an Alicorn now! How is that even possible?! Does your species have a sudden evolutionary change, and why are your wings angled? You must be considered a princess now! You should get a cane with your face on it! I think it would be the most hilarious thing I would ever see!" "_Even his attitude is stranger than usual. I have no idea how to help him in his current state! Maybe if I just tell him about Derpy being concerned, maybe he'll explain. After all those two ponies have been through together, I wouldn't doubt his loyalty to Derpy."_ Twilight thought to herself. "Doctor, Derpy is concerned about you! You've been in your TARDIS for months on end, not leaving even once to take a break!" "Don't be ridiculous, Twilight! It's only been a few days!" The brown stallion responded. "LOOK AT YOURSELF! Your mane is as tangled and unkempt as the Everfree Forest, your coat is a completely darker shade of brown, and you've almost made little to no sense as soon as you walked in!"

After Twilight's rant, The Doctor finally came to his senses a little and took a few minutes to look at himself in a nearby mirror. He was shocked at the stallion staring back through it. "_Twilight's right. What few days I spent in the TARDIS must've been months out here!" _After examining his unkempt self, The Doctor bowed his head down sorrow and began to apologize. "I-I'm sorry, I wasn't aware that it's been that long. When you spend a lot of time in the TARDIS, a few hours could feel like mere seconds. Honestly, I didn't know how long I was actually in there." After hearing this, Twilight regretted yelling at him the way she did and apologized as well. "Now that you've come to your senses, could you tell us the reason behind your research? What's so important about the sun and moon cycles?" "Before I came to this planet, there was a friend I had. Rose Tyler was her name. One day while we were travelling, we were trans-matted onto different TV game shows on a space station, which was controlled by Daleks secretly. In order to save everyone, Rose looked into the Time Vortex itself, gaining god-like powers. This transformed her into Bad Wolf- an incarnation of the Vortex with a desire to help, no matter what the cost." The Doctor said. "Isn't that a good thing, though Doctor?" Derpy asked. "The problem is no one person can have that much power coursing through them, not even Time Lords such as myself. So, in order to save her, I had to take that power within me and give it back to the TARDIS, which acted as a conduit of that energy; That's how it travels through time and space. The few seconds I had that power coursing within me was also enough to nearly kill me. That's when I regenerated for the 10th time." Both mares listening to this story began to understand why the TARDIS was a dangerous thing if an enemy got a hold of it. "Before I took the power away from Bad Wolf, she said something that's been itching at me ever since I came to Equestria." "What did she say, Doctor?" Both ponies asked simultaneously. "'I control the sun and moon, but why do they hurt?' For 80 years, that quote was meaningless to me, just an echo from the past, but now I get it! There must be something that's going to happen to your princesses and I think the day and night cycles might have something to do with it." "*gasp* I just realized, Doctor! Before I came to get you, I received a reply letter from the Princesses and it said there was a threat made on Canterlot." The Doctor had a smile on his face after hearing this. "Then what are we waiting for? Let's Go!"


	2. Chapter 1

**Chapter 1: History's Repeat**

_A few minutes later, just outside Canterlot; The Doctor, Derpy and Princess Twilight begin to seek out Princesses Luna and Celestia to investigate the mysterious threat discussed in their letter to Derpy._

"Twilight, you're close to the princesses. Is there anything they might've said or done to indicate what sort of danger they would be in?" The Doctor asked the purple alicorn. "I have no idea, Doctor. The last time I saw them was after we restored the Tree of Harmony to stop the Everfree Forest from invading. Since then, they've been putting some distance away from any citizens of Equestria. They don't even visit me and my friends from Ponyville anymore." With this new information, The Doctor formulated new thoughts and ideas that might explain their unsociable behavior. "_What if they were traumatized by what they experienced in the Everfree? No, that can't be right. I've seen the way they stand proud during times of distress. Maybe, just maybe this threat is from another world and they were the targets? That's it! They've isolated themselves to protect their citizens!"_ After he was done with his thoughts, a smile of determination dawned on his face. "Derpy, hand me that letter." "Why, Doctor?" She asked. "If I am correct, this letter is a cipher to tell us the threat the princesses are facing. If they've been isolating themselves, it wasn't because of standard precaution but instead are the targets of something alien and way beyond their capability to protect their citizens from the danger they are facing. Twilight, is there any secret Canterlot code the princesses used in the past to relay messages in times of distress?"

"In the diary of the princesses recovered from their old castle mentions a riddle game Luna and Celestia played. Since they were heavily surrounded by guards in separate rooms at nighttime, they would send letters that didn't make sense if a guard read them, but if you took the 7th word of the second sentence in the letter and read them with the first 8 words of the next sentence, the riddle would be solved."

"That's it!" The Doctor exclaimed. "If we apply that same cipher onto Derpy's letter, it says 'help, a threat has been claimed on our lives.' Now that to me sounds like they need us more than ever! Come on, it shouldn't be that hard to find the two most powerful beings in Equestria."

_A few minutes later, in the TARDIS…_

"Thanks to the cipher, now we can trace the message back to its source." said The Doctor. "How can it do that?" Twilight asked. "Oh, it's completely impossible to explain right now." The Doctor began to look serious. "If this threat is too dangerous even for me to handle, I need you two to go to the TARDIS. It would take an entire supernova to break through those doors and the last thing I want to happen is you two getting hurt, or worse." The engines stopped their trademark wheezing groan, indicating to it's passengers that they arrived at their destination.

The Doctor, Derpy, and Twilight opened the doors and saw they were in the throne room, but something felt off to the three. Sitting on the throne was Celestia, but she kept staring blankly in front of her. "Are you alright, Princess?" The Doctor asked. "Oh? Are you new here? I always like to see new faces!" The three ponies became confused at this response. "Celestia, don't you recognize me? It's Twilight, your faithful student!" Now the Princess dawned a confused look. "You can't possibly be my student! My student is Sunset Shimmer!"

"How many years have you been ruling so far?" The Doctor asked.

"For about 900 years. Why do you ask?" Celestia said.

"This is exactly what I thought. Someone has opened her past up like a picture book!"

"What does it mean, Doctor?" Derpy asked. "It means the 'danger' they were talking about was this exact thing happening! The reason they've isolated themselves was to prevent any reminders that might give our unknown foe what they were looking for, which means…" Suddenly, the scene around them began to change. Celestia was still there, but seemed older and more familiar with the 3 ponies standing before her. "Oh hello, Doctor! Is something wrong?" The ruler of Equestria asked. Other than The Doctor, the ponies in the room seemed very confused. "Celestia, if you can hear me, give me a sign. Try to remember something, anything!" The illusion before them began to distort, revealing Celestia in real time for a brief moment. "Doctor, help me! AHHH!" The seriousness of the situation now dawned on the two mares. "Celestia! Doctor, how do I save my mentor? Please tell me!" Twilight exclaimed in a frightened and worrisome voice. The only thing he could do was turn his head in shame. "I-I can't, Twilight. As much as I wish I could, there is nothing I can do that wouldn't harm you or the Princess. What we need is somepony who can synchronize Celestia's memories in the proper order."

The two mares now looked confused. "What I mean is we don't have direct experience with her past" he tried to explain. "Twilight, even with that memory potion you received from Zecora you still have memories of her later years, just before the defeat of Nightmare Moon. And as for me and you Derpy, we haven't directly intervened with her memories or her mind. We just lent a helping hand, that's all. Our best bet is to search for her sister, Luna."

They began to understand how much of a risk and a gamble it would be to just repair the memories all on their own. Now that they were all on the same page, the three began to look for Princess Luna in whatever condition she was in.

_In a universe unknown to the three companions, a plot began to form…_

"PHASE ONE COMPLETE, DALEK SUPREME." A Dalek said.

" BEGIN PHASE TWO IMMEDIATELY." The Dalek Supreme stated. "CYBERMEN, WE ARE IN TEMPORARY ALLIANCE UNTIL THE ULTIMATE GOAL IS RECEIVED. IS THIS DIRECTIVE UNDERSTOOD TO YOU?" In front of the Dalek Supreme, a hologram image formed of the Cyber Controller. "The Directive has been stated and assessed. The alliance will be formed. Cybermen are now under control of Daleks until primary directive has been neutralized. Phase Two is commencing."

A battle map on both Cyber and Dalek ships were displayed with 3 blips in the center of what looked like a labyrinth. Suddenly with the push of a button, the labyrinth rotated and formed a new path for these 3 blips to follow. Strangely enough, at the other end of this new path was a slightly larger 4th blip.

_At the same moment in the Castle…_

"Shh. Do you hear that?" The Doctor said. Both Twilight and Derpy stared at him and simultaneously asked "Hear what?" Suddenly, the room began to rumble and shake, causing the roof to crack and chunks to fall. All of a sudden, the rumbling stopped. "Interesting. Twilight, can you fly through one of the holes in the roof and tell us what you see?" The Doctor asked. She did as told and flew through one of the many holes now adorned in the ceiling. "Good. Now tell me, what do you see?" Twilight looked around and to her astonishment saw a huge maze! "It's a maze!" yelled Twilight. "A giant maze! It must stretch for thousands of miles! But, how is that possible?" She flew down after describing the labyrinth to the other two. "Just as I thought." The Doctor said. Derpy looked frightened and scared. "Doctor, where are we? Is this the Canterlot we know?" She asked. "No. It's just a clever ruse to get me to play. Well I'm not playing, you hear me?! I'm not budging!" he yelled. "Derpy, Twilight, we're in a labyrinth designed by my predecessors, the Time Lords. It's an endless maze that can be manipulated and changed however they please.

"But this shouldn't be possible! This technology should've been lost!"

"What do you mean, Doctor?" Twilight asked. "What I mean is the last of these Gallifreyan Time Mazes was destroyed when my race went to war with-". By that point, The Doctor realized who put them in this death trap. "With who, Doctor?" both the worried ponies shouted. He then took a big gulp and said "With the Daleks of Skaro."


	3. Chapter 2

**Chapter**** 2: Trapped**

"Are you saying that the Daleks are responsible for capturing the two most important ponies in Equestria?!" Shouted Twilight. "Unless the Time Lords are returning, the chances are high that they abducted Luna and Celestia and put them in this prison. I don't know how they've recovered this maze, but what I do know is the threat could be extremely dangerous either way." The Doctor thought for a moment, and looked around the room. _"Weren't there 3 doors before I heard that noise? They couldn't have figured out the controls that fast! Whoever we're facing, whether it is Daleks or Time Lords, someone or rather something is guiding them and until I figure that out, we're all just mice in a maze trying to find the cheese at the end._" He thought to himself. "It looks like that tremor we felt was the maze coming online, and the first change of routes was to this room. It looks like the only way now is forward." With that, they ventured down the only path presented to them. As the ponies were moving forward, they all began to feel an emotion arise and become stronger with every step. Each emotion was different for the ponies. For The Doctor, the emotion was Fear; Derpy's was Anger, and Twilight's was Curiosity. The Doctor caught on to this. "I'm sure you two have noticed as well."

"Noticed what?" Twilight replied. "Our emotions have been tampered with. Each emotion you feel that is stronger than the others are designed to slow us down and have us quarrel with one another. Twilight, can you think of any spell to counteract with this?" The Doctor said. "Actually, I might. During Queen Chrysalis' invasion, Cadence used a love spell. If I could only find the original spell, I might be able to adapt it to counteract our imbalanced emotions. The problem is, only Celestia, Luna, and Cadence know the spell, one of them is being tortured, and the other two are probably still at home! Oh, Celestia! I have no idea what to do!" The Doctor saw something that slightly startled him. "Twilight, you might have a chance to get that spell. Look!" He pointed to the end of the hallway, and to all three as a surprise was Princess Luna, but something seemed different. "LUNA! Thank Celestia, you're okay!" Twilight said as she ran to her ruler and friend. Suddenly, a dark blue wisp of magic was shot toward the sprinting Princess and was followed by a scream of pain. "INSOLENT FOOL! Luna is no more! For I am Nightmare Moon! MUHUHUAHAHA!"

In a flash, The Doctor stood in between the injured Twilight and Nightmare Moon. With a quick flick of his Sonic Screwdriver, he shot a Paralyzing Sonic-wave towards the malicious alicorn, stunning her temporarily. "Twilight, I need you to use that memory spell for your friends on Luna! It's the only way to bring her back at this point!" With a pain, she nodded and began to cast the spell. At the same time, The Doctor increased the frequency on his Sonic to Incapacitate Nightmare Moon's horn and muscle functions. "Now!" The Doctor called out and Twilight released the spell to Luna, making her remember the memories of the past few months, knocking her out after it was done. When she regained consciousness, Luna remembered what happened. "Doctor, This was a trap to lure you here!" she burst out.

"Yes I know, Luna. My suspicions arose when nopony came to escort me. Last time, your sister had me escorted by her royal guard, remember?" The Doctor said.

"Now that you recall it, I do remember. It was around the time we first met, and you were mesmerized by how I could raise the moon, just like how my older sister could raise the sun. Is that why we're here, Doctor? Is it because of our abilities to raise and lower celestial bodies?"

"I'm afraid so, Luna. This place we're in, it's full of Time Lord Devices and Technology. Any number of them can be used to harness your power. With yours and your sister's combined, it would rival the powers of a god." The Doctor looked around for a moment for any disguised listening devices. After he found a few, he used his Sonic Screwdriver to turn them off temporarily. "Listen, and listen carefully: whoever set this trap is incredibly intelligent. Only a small portion of the galaxy knows of my race. Even fewer know where to get their hands on a Time Maze. Your discovery, Luna, was planned. When the engines started, neither Twilight nor Derpy could hear them because it was meant to be heard only to me. You two were meant to be left clueless. After the ceiling collapsed and you revealed the maze, Twilight, upon instinct I looked around for any exits. If they wanted to kill us, why not seal off escape routes by removing the doors? No, this was planned very carefully. They _wanted_ me to find Luna. They _needed _me to get cut off from the TARDIS. What this means is that whatever is at the end of this twisted path, will either try to kill us, or whoever it is will try to get us to help them." The hidden microphone turned back on and prevented The Doctor from explaining further. "_I'm sorry, Twilight, it appears the way back to the TARDIS is blocked…_" He said with an extremely exaggerated voice. The other 3 ponies became confused, so The Doctor nudged them with a worried look on his face. As soon as they noticed what he was doing, they understood and played along.

_ After a few minutes of walking through the Time Lord maze, the 4 ponies came across something that blocked their path…_

"Doctor, what is that thing?" questioned Twilight Sparkle. What stood before them was a massive wall, which was brimming with magical energy. The Doctor was about to scan it with his Screwdriver when Luna stopped him. "Don't do that, Doctor. You'll only make it stronger." She said.

"And might I ask why?" he replied.

"If you value your life, you will listen to me. This wall is known as a Gate of Tartarus, or at least a prototype." Twilight's jaw nearly dropped when she heard this. "You mean to tell me that THIS is just a prototype?! It's huge! The actual one has to be at least twice the size!" Luna nodded. "Yes, Twilight, the actual one is much bigger, but it matters not right now. Back when Celestia and I were ruling for the first time, we devised a plan to store all of the threatening beasts that are known as myths and legends nowadays. At first, we thought putting them on either the sun or moon would be enough, but after a while, some of the more magically potent ones teleported back to the planet and again started to wreak havoc. Error after error we tried numerous ideas that expended the royal treasury multiple times, putting the nation in several periods of economic collapse and poverty. Then, a very powerful wizard came and offered a new solution. You have encountered his ancestor, Twilight. The one you call Trixie, I believe." She explained. Twilight was suddenly filled with envy towards Trixie. "So that's why she calls herself 'great and powerful'?" Twilight frustratingly said. "Yes. He often talked about his great granddaughter with a sort of pride for her. It only made sense that she called herself those things because of her heritage. After all, her great grandfather was responsible for the design of the Gate of Tartarus. But moving on from the subject, he devised a plan for powerful wizards and mages to work together with esteemed scientists. With the geographical knowledge of volcanos and the expertise of magical barriers, the two professions unlikely paired up and began construction of prototypes for this 'Pit of Tartarus'."

She continued. "After many attempts, they successfully created one. What happened to the prototypes was unknown, until now."

"Wait a minute, how do you just lose a door this size?!" Exclaimed The Doctor.

"We don't know! Back then, we were a very unorganized princess and as such we just lost track of things!" Luna replied frustratingly.

"In that case, we'll just have to find a way to tear it down." The Doctor said. "That's the thing," Luna started, "the more you try to destroy it, the stronger it gets. Even the slightest scratch will trigger its defensive mode. The earliest of prototypes, such as this one also had a major defect: its magical barrier wasn't properly executed, so in combination with its defensive capabilities, the barrier sapped any spell caster of their energy if they so much as tried to mess with the barrier, resulting in the death of the caster. That's why I stopped you from using your Sonic. That same barrier doesn't know the difference between technology and magic. It probably thinks your Screwdriver is nothing more than a fancy looking wand."

The Doctor thought for a moment. _"So there were two paths we could've had: we could have gone back to the TARDIS and gather any resources we could before we even ventured this deep, and the one where we just started breaking down a new path for us to cross while the walls were still thin and weak. Looking at our options now, it seems there is only one left, and they won't like what I am about to do…"_


End file.
